Interesting Articles
10 and 11.]] Foldit in the news *"Origami Revolution" on Nova TV show features David Baker with brief glimpses of Rosetta@Home and Foldit. (Broadcast on PBS in the US February, 2016.) *How online gamers are solving science's biggest problems Review of Foldit and other online citizen-scientist vehicles. Features a glimpse of the rarely photographed Zoran Popovic. (January, 2014) *These {cool} games let you do real-life science Earlier review of Foldit and its peers. (May, 2013) General science *The Shape-Shifting Army Inside Your Cells Discussion of how "intrinsically disordered proteins" violate the assumption that a protein has a single shape, known as Anfinsen's dogma. (January, 2017) *Novel 'nano-reactor' pumps out hydrogen biofuel Report describing a bio-engineered virus the produces hydrogen gas. (January, 2016) *3D images reveal the body's guardian against urinary infection Report on the discovery of the crystal structure of uromodulin. (January, 2016) *Scientists discover a trigger of Alzheimer's disease (March, 2016) *Protein Structure and Structural Bioinformatics(October, 2016) *Study offers a new route to design the 'cellular machines' needed to understand and battle diseases (May, 2016) *This protein designer aims to revolutionize medicines and materials (July, 2016) *A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins (October, 2010) *Principles for designing ideal protein structures(November, 2012) *Determining crystal structures through crowdsourcing and coursework (September 2016) The contribution of Foldit players to Scientific Results All Foldit players participate in a scientific investigation. Whatever their contribution (from folding to giving feedbacks or giving tips to other or sharing intermediate solutions). As "citizen scientist", they contribute directly to some mass data collections on likely protein structures (from a mass of results, top scoring solutions are analyzed as the best promising, but also "shared to scientists" ones and even low scoring ones for statistical analyses). They are also observed as players and/or citizen scientists. From this point of view, they are themselves "objects of science" They are the objects of social or technical studies on "gamification", games, social sciences, human/machine interface, artificial intelligence etc. Aside of pure fun in competition, "contributing to Science" has been reported as one of the highest motivation of Foldit players. The contribution of Foldit players is often acknowledged by the researchers in their blogs and science chats, as well as by many authors who quote Foldit as a famous example of complex and difficult "serious game" or "game with purpose". But very high level scientific visible results are rare enough to be quoted here. The papers bellow are papers where Foldit players contributed significantly to Scientific advances, either as co-authors or as "co-subjects" of studies that have reached high level scientific publications. * Firas Khatib, Ambroise Desfosses, Foldit Players*, Brian Koepnick, Jeff Flatten, Zoran Popović, David Baker, Seth Cooper, Irina Gutsche, Scott Horowitz (*Alan Coral, Alexander Boykov, Alexander Paul Brough, Allen Richard Lubow, Alyssa Joy Higgins, Дмитрий Сергеевич Голощапов, Bartosz Kaszubowski, Binyou Wang, Brett A. Burkholder, Brian M. Lee, Bruno Kestemont, Catherine R Landers, Charles Coqueret, Charles Cusack, Charles David Coleman, Cheryl Greenwell, Christiaan Narinx, Christopher D. Eastlake, Coby Walker, Dahlia Dry, Dave Trownsell, David Murray, Douglas Craig Wheeler, Ernest Webb, Gary O. Gross, George Victor McIlvaine, Gregory T. Hansen, Harald Feldmann, Heidemarie Karin Fuentes, Istvan Kovanecz, Jake Fisher, Jami Lynne Borman, Jasper A. Diderich, Jeffrey M Canfield, Joanne Mitchell, John Michael Joseph McMahon, John Mitch, Jonas Schinkler, June M Brownlee, Justin Wangying Lam, Keith T. Clayton, Kenneth E. DeFord, Kevin Dale Wells, Kirk Joseph Abbey, Larry C. Withers, LaVerne Poussaint, Leanne Riki Cheever, Lennart E. Isaksson, Linda Wei, Luis Alonzo Villagomez, Lynn Carpenter, Manasa Sharma, Marco Post, Michael Krapukhin, Patrick Brady, Patrick John Rabaja Camarador, Pavel Varlashin, Pavlo Denys, Peter John Triggiani IV, Ricardo Oliveira da Silva, Robert Gamble, Robert Leduc, Roman Madala, Savas Pashalis, Scott Shnider, Sebastian Graf von Matuschka, Sergey Pinyaev, Stefan Kunert, Steven A. Schwegmann, Susan Curry Kleinfelter, Sven Michael Holst, Thomas Bausewein, Thomas J. George, Timotheus J.A. van der Laan, Todd Burckin, Ulas Yeginer, Usman Rehman, Vasiliy Sidoruk, Vedran Sabljak, Vera Simon, Walter Barmettler), Building de novo cryo-electron microscopy structures collaboratively with citizen scientists, PLOS Biology 17(11): e3000472 (2019). *Brian Koepnick, Jeff Flatten, Tamir Husain, Alex Ford, Daniel-Adriano Silva, Matthew J. Bick, Aaron Bauer, Gaohua Liu, Yojiro Ishida, Alexander Boykov, Roger D. Estep, Susan Kleinfelter, Toke Nørgård-Solano, Linda Wei, Foldit Players (A.C.L. Heessels, Adam Heinermann, Alan Coral, Alekhya vytla, Alessia Visintin, Alex James Bubar, Alexander Boykov, Alexander Uriel Valle Perez, Alireza Nematollahi, Alison Kahl, Alison MacMillan, Allen Richard Lubow, Amy Blumke, Andrea Kis, Andrei Kolchugin, Andrei Mikhailovich Zhirov, Andrew John Ardill, Andrew Taylor Maxwell, Andrew Wilzman, Angelo Papagelos, Anthony Naquin, Aqib Feroz Zakaria, Artak Kalantarian, Bartosz Kaszubowski, Belinda Lackersteen, Benjamin A. Mooso, Benjamin Chagot, Benjamin Keith Myers, Beverly R Haight, Bora Tastan, Boris Kamenik, Boris Uitham, Brandon G Roy, Brandon Lin, Brian Echols, Brian Edward Lorenz, Brian J Blair, Bruce A Blair, Bruno Kestemont, Caitlyn Singam, Callen Joseph Bragdon, Carl Vardeman, Carlo Stephen Salerno, Casey Blokzyl, Casey Comisky, Catherine Lousie Hayman, Catherine R Landers, Cathy Zimov, Cerullo Dario, Charles Cusack, Charles David Coleman, Charles Robert Painter, Christian Berg, Christian Chauvin, Christophe Garnier, Christopher Walther, Christopher William Ince Jr., Craig Perry Brownell, Dale G. Mack, Damien, Jean-Michel Rondeau, Daniel Jon Anthony Buske, David Carl Lefkowitz, David Carman, David Dahlen, David G. Nye, David Mattingly, David Rhodes, David William Glover, Denis Štingl, Dennis Schroder, Dmitrii Malaniia, Dominik Stadler, Douglas Craig Wheeler, Dr. Vera Simon, Dustin Wortmann, Elie Cali, Emanuele Chisari, Emmanuel Croze, Eric Lim Jit Kai, Erik M Schmidt, Farah Rezae, Felix Fischer Marques, Ferenc Lengyel, Flavian Tabotta, Floyd Orville Martin, Jr, Franco Padelletti, Frederick James Austin, Gabriel Roper, Gary O. Gross, George Victor McIlvaine, Gil Beecher, Gioele Ciaparrone, Gregory Scott Muhs, Gregory T Hansen, Guido de Jong, Guy Ykman, Hans van den Hof, Harald Feldmann, Heidemarie K Fuentes, Hochart Xavier, Ian Kuula Ross, Imara Beattie, Iryna Zaporozhets, Istvan Kovanecz, Jacob North, Jae Hyun Choi, Jakub Halamek, James Absalom Longino III, James Christopher Pino, James Paul Crosby, Jami Borman-Allen, Jan Bartoň, Jan Pluta, Jan Vodražka, Jane Elizabeth Norrgard, Janae Loree Hammon, Janet Tollenaar, Jared Glenn Hanson, Jason Cam Truong, Jasper A. Diderich, Jeanne Kanfer, Jeffrey Michael Canfield, Jeffrey Photakis, Jesse David Slone, Jesse Moe, Ji-hwan Ma, Joanna Madzio, Joanne Mitchell, Joao C. Sequeira, Johannes Carl Gabl, John Davies, John Mitch, John William Kennedy III, Johnathan Altenbeck, Jon Petur Gunnarsson, Jonas Schinkler, Jorge Ramon Cantero Pinanez, Jorn Loots-Boiy, Joseph Hobbs, Joshua Burbach, Joyce Liu, Juan Francisco Bada Juarez, Juan Luis Larroucau de Magalhaes-Calvet, Judith Oremen, June M Brownlee, Kalman Takacs, Kat Meltzer, Kathleen Diane Harper, Keith T. Clayton, Kenneth E. DeFord, Kevin Dale Wells, Kevin F. Scully, Kevin G Yang, Kevin Michael Gildea, Kirk J. Abbey, Kristen Lee Kohli, Krzysztof Orliński, Kya Roberts, Kyle Cooley, Kyle Stenner, Kylie May Cheng, Kyusik Han, Larry C. Withers, Larry Cacao Manalo Jr., Lars Rose, LaVerne Poussaint, Leanne Riki Cheever, Lennart E. Isaksson, Lilium Carlson, Linda Wei, Lindsay Neumann, Linus C Villanueva, Lori A. Miller, Lucas Robert Von Borries, Luke Kramer, Luke Ryan Fisher, Lynn Carpenter, Ma. Donie Jane M. Merca, Maciej Petelski, Manasa Sharma, Manfred Ehresmann, Manuel Goldner, Manuel Ricci, Marcus Belcastro, Marek Leniec, Marie Suchard, Mark Richard Lawrence, Mark Stewart Binfield, Marnix Z. Meijer, Martin G. Szew, Mateusz Naściszewski, Matthew "Mookie" Thayer, Matthias Gaebel, Maurizio Locatelli, Maya Tselios, Michael Allan Lewis, Michael Bohme, Michael D. Cassidy, Michael Fagiola, Michael Geoffrey Bond, Michael John Klein, Michal Stepniewski, Mirjam van Delft, Miroslav Kolshev, Moamen Mahmoud Elmassry, Mussini Andrea, N Mark Milton, Nader Angelo Simone Baydoun, Nandi Solomon Ravi Bhushan, Neil Cameron, Niklas Alexander Lars Goernitz, Noah Benevides, Noah Chen, Norah Kathleen Kerr, Nova Barlow, Oak Shannon, Olusegun Abayomi Onanuga, Owen Yin, Oyvind Odegard Fougner, Paryohin Danil Alexsandrovich, Pascal Wolfteich, Patrick Brady, Patrick John Rabaja Camarador, Paul Gummersall, Paul Michael Thomson, Pavel Plaschinsky, Paweł Sznajder, Peter Gajar, Peter John Triggiani IV, Philippe Castera, Phillip Burghardt, Pietro Bongini, Rafał Kiełbus, Renee Brody, Renton Braden Mathew Innes, Ricardo Oliveira da Silva, Ricky Buchanan, Rita Dachner, Robert Dumitru, Robert Fraser, Robert Leduc, Robert Paul Catherina, Robert Paul Gamble, Roman Madala, Ruth Ann Buzzi, Ryan D Moore, Ryan DeWitt, Sachin Agrawal, Samuel Britton Newhouse, Sarah Krzyminski, Scott Boyd, Scott J. Zaccanelli, Scott Shnider, Sean Mooney, Sergey Kuznetsov, Sergio Burillo-Sanz, Sharon deBoisblanc, Sherry Bermeo, Sidoruk Vasiliy, Slava Stalina Butkovich, Spencer Bruce Hudson, Stephanie Williams, Stephen Denne, Stephen John Plumb, Steven A. Schwegmann, Sumanth Ratna, Susan Kleinfelter, Frisno Bostrom, T.J.A. van der Laan, Talluri Sekhar, Tatiana Malygina, Thomas Bausewein, Thomas J George, Tobias Scherf de Almeida, Todd Burckin, Toke Norgard-Solano, Tom Espen Pedersen, Tomaš Vondrovsky, Tomasz Głąb, Travis MacKinnon, Trevor M Nolan, Tyler Jeffrey Russell, Ulas Yeginer, V. Glasser, Valerie Hellmer, Venkata Saroja Rani Betina, Vincent Chiu, Vincenzo Brancaccio, Vitali Drozd, Vitor Adriano Dantas Paranhos, Vojtech Kapras, Walter Barmettler, Warwick Pulley, Wayne Turnbull, William P Dunnam, William Scott Wright, Wyatt Reed Lansford, Yigitcan Aksari, Yoan Anthony Skander Gaiji, Youngwan Kim, Yu-Tian Xiao) , Gaetano T. Montelione, Frank DiMaio, Zoran Popović, Firas Khatib, Seth Cooper & David Baker, De novo protein design by citizen scientists, Nature, volume 570, pages 390–394 (2019) *Chen Keasar, Liam J. McGuffin, Björn Wallner, Gaurav Chopra, Badri Adhikari, Debswapna Bhattacharya, Lauren Blake, Leandro Oliveira Bortot, Renzhi Cao, B. K. Dhanasekaran, Itzhel Dimas, Rodrigo Antonio Faccioli, Eshel Faraggi, Robert Ganzynkowicz, Sambit Ghosh, Soma Ghosh, Artur Giełdoń, Lukasz Golon, Yi He, Lim Heo, Jie Hou, Main Khan, Firas Khatib, George A. Khoury, Chris Kieslich, David E. Kim, Pawel Krupa, Gyu Rie Lee, Hongbo Li, Jilong Li, Agnieszka Lipska, Adam Liwo, Ali Hassan A. Maghrabi, Milot Mirdita, Shokoufeh Mirzaei, Magdalena A. Mozolewska, Melis Onel, Sergey Ovchinnikov, Anand Shah, Utkarsh Shah, Tomer Sidi, Adam K. Sieradzan, Magdalena Ślusarz, Rafal Ślusarz, James Smadbeck, Phanourios Tamamis, Nicholas Trieber, Tomasz Wirecki, Yanping Yin, Yang Zhang, Jaume Bacardit, Maciej Baranowski, Nicholas Chapman, Seth Cooper, Alexandre Defelicibus, Jeff Flatten, Brian Koepnick, Zoran Popović, Bartlomiej Zaborowski, David Baker, Jianlin Cheng, Cezary Czaplewski, Alexandre Cláudio Botazzo Delbem, Christodoulos Floudas, Andrzej Kloczkowski, Stanislaw Ołdziej, Michael Levitt, Harold Scheraga, Chaok Seok, Johannes Söding, Saraswathi Vishveshwara, Dong Xu & Foldit Players consortium (Ahmet Caglar, Alan Coral, Alison MacMillan, Allen Lubow, Barbara Failer, Bruno Kestemont, Catherine R. Landers, Charles Robert Painter, Christophe Garnier, Claudine Sellin, Dietmar Janz, Douglas Craig Wheeler, Vera Simon, Dylan M. Flear, Emmanuel Croze, George Victor McIlvaine, Gil Beecher, Gordon Lawrie, Guy Ykman, Harald Feldmann, Heidemarie K. Fuentes, Hosokawa Terumasa, Istvan Kovanecz, James Absalom Longino III, Jan Hendrik Nijland, Jasper A. Diderich, Jeffrey M. Canfield, Jesper Eriksson, Jesse David Slone, Joan Goldsworthy Appel, Joanne Mitchell, John Mitch, Jorn Loots-Boiy, June M. Brownlee, Karsten Wilson, Keith T. Clayton, Kenneth E. DeFord, Kirk J. Abbey, Larry Withers, Linda Wei, Lloyd Ives, Lori A. Miller, Lynn Carpenter, Manasa G. Sharma, Manuel Ricci, Mark Stewart Binfield, Matthew John Davids, Matthias Gaebel, Michael D. Cassidy, Michael Fagiola, Michael Pfützenreuter, Nova Barlow, Peter John Triggiani IV, Renton Braden Mathew Innes, Robert Leduc, Rodrigo Luccas Corrêa dos Santos Gomes, Rosemarie L. R. Morneau, Scott J. Zaccanelli, Susan C. Kleinfelter, T. J. A. van der Laan, Thomas Bausewein, Thomas J. George, Varichev Mikhail & Walter Barmettler) & Silvia N. Crivell. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Nature Scientific Reports volume 8, Article number: 9939 (2018) *Marisa Ponti, Igor Stankovic, Wolmet Barendregt, Bruno Kestemont, Lyn Bain, Chefs Know More than Just Recipes: Professional Vision in a Citizen Science Game. Human Computation Vol 5 (2018), 1-12 *Ponti, M., Stankovic, I., Barendregt, W., Kestemont, B., & Bain, L. Chefs know more than just recipes: professional vision in a citizen science game SocArXiv. (2017, March), doi:10.31235/osf.io/yqw6g. *Scott Horowitz, Brian Koepnick, Raoul Martin, Agnes Tymieniecki, Amanda A. Winburn, Seth Cooper, Jeff Flatten, David S. Rogawski, Nicole M. Koropatkin, Tsinatkeab T. Hailu, Neha Jain, Philipp Koldewey, Logan S. Ahlstrom, Matthew R. Chapman, Andrew P. Sikkema, Meredith A. Skiba, Finn P. Maloney, Felix R. M. Beinlich, Foldit Players, University of Michigan students, Zoran Popović, David Baker, Firas Khatib & James C. A. Bardwell. Determining crystal structures through crowdsourcing and coursework. Nature Communications 7, Article number: 12549 (2016), doi:10.1038/ncomms12549 *Curtis, Vickie Online citizen science projects: an exploration of motivation, contribution and participation. PhD thesis The Open University (2015). *Marisa Ponti, Thomas Hillman, Igor stankovic Science and Gamification: The Odd Couple? ACM Digital Library (2015) *Marisa Ponti, Igor Stankovic Scripts in a Gamified Crowdsourcing Approach to Do Science Presented at “Examining the Essence of the Crowds: Motivations, Roles and Identities”, a workshop at ECSCW 2015, September 19, 2015, Oslo, Norway Conference contribution. (2015) *Dun-Yu Hsiao, Seth Cooper, Christy Ballweber and Zoran Popović. User behavior transformation through dynamic input mappings. Proceedings of the 9th International Conference on the Foundations of Digital Games (2014). *George A. Khoury, Adam Liwo, Firas Khatib, Hongyi Zhou, Gaurav Chopra, Jaume Bacardit, Leandro O. Bortot, Rodrigo A. Faccioli, Xin Deng, Yi He, Pawel Krupa, Jilong Li, Magdalena A. Mozolewska, Adam K. Sieradzan, James Smadbeck, Tomasz Wirecki, Seth Cooper, Jeff Flatten, Kefan Xu, David Baker, Jianlin Cheng, Alexandre C. B. Delbem, Christodoulos A. Floudas, Chen Keasar, Michael Levitt, Zoran Popović, Harold A. Scheraga, Jeffrey Skolnick, Silvia N. Crivelli and Foldit Players. WeFold: a coopetition for protein structure prediction. Proteins (2014). *Christopher B. Eiben, Justin B. Siegel, Jacob B. Bale, Seth Cooper, Firas Khatib, Betty W. Shen, Foldit Players, Barry L. Stoddard, Zoran Popović and David Baker. Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature Biotechnology (2012). *Erik Andersen, Eleanor O'Rourke, Yun-En Liu, Richard Snider, Jeff Lowdermilk, David Truong, Seth Cooper and Zoran Popović. The impact of tutorials on games of varying complexity. Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (2012). *Firas Khatib, Seth Cooper, Michael D. Tyka, Kefan Xu, Ilya Makedon, Zoran Popović, David Baker and Foldit Players. Algorithm discovery by protein folding game players. Proceedings of the National Academy of Sciences of the United States of America (2011). *Miroslaw Gilski, Maciej Kazmierczyk, Szymon Krzywda, Helena Zábranská, Seth Cooper, Zoran Popović, Firas Khatib, Frank DiMaio, James Thompson, David Baker, Iva Pichová and Mariusz Jaskolskia. High-resolution structure of a retroviral protease folded as a monomer. Acta Crystallographica (2011). *Firas Khatib, Frank DiMaio, Foldit Contenders Group, Foldit Void Crushers Group, Seth Cooper, Maciej Kazmierczyk, Miroslaw Gilski, Szymon Krzywda, Helena Zábranská, Iva Pichová, James Thompson, Zoran Popović, Mariusz Jaskolski and David Baker. Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature Structural and Molecular Biology (2011). *Seth Cooper, Firas Khatib, Ilya Makedon, Hao Lu, Janos Barbero, David Baker, James Fogarty, Zoran Popović and Foldit Players. Analysis of social gameplay macros in the Foldit cookbook. Proceedings of the 6th International Conference on the Foundations of Digital Games (2011). *Seth Cooper, Firas Khatib, Adrien Treuille, Janos Barbero, Jeehyung Lee, Michael Beenen, Andrew Leaver-Fay, David Baker, Zoran Popović and Foldit Players. Predicting protein structures with a multiplayer online game. Nature (2010). *Seth Cooper, Adrien Treuille, Janos Barbero, Andrew Leaver-Fay, Kathleen Tuite, Firas Khatib, Alex Cho Snyder, Michael Beenen, David Salesin, David Baker, Zoran Popović and Foldit players. The challenge of designing scientific discovery games. Proceedings of the 5th International Conference on the Foundations of Digital Games (2010). Category:The game